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843 Molecular Subtypes in BCR::ABL1-Positive ALL Are Defined By Cellular Origins and Cooperating Genomic Events

Program: Oral and Poster Abstracts
Type: Oral
Session: 618. Acute Lymphoblastic Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: Novel Disease Subclassifications and Clinical Prognosis
Hematology Disease Topics & Pathways:
Research, Translational Research, genomics, Biological Processes, Technology and Procedures, pathogenesis, machine learning, omics technologies
Monday, December 11, 2023: 3:15 PM

Lorenz Bastian1,2*, Thomas Beder1*, Malwine Barz, PhD2,3*, Sonja Bendig2,4*, Lorenz Bartsch3*, Wencke Walter, PhD5*, Nadine Wolgast2*, Björn Brändl6,7*, Christian Rohrandt8*, Björn-Thore Hansen1*, Alina M. Hartmann2,3*, Katharina Iben2,3*, Miriam Bultmann3*, Johannes Zimmermann9*, Michael Wittig10*, Guranda Chitadze2*, Martin Neumann2*, Folker Schneller, MD11*, Walter Fiedler, MD12, Björn Steffen, MD13*, Matthias Stelljes, MD14, Christoph Faul, MD15, Stefan Schwartz, MD16*, Franz-Josef Müller17,18*, Gunnar Cario, MD2,19*, Lana Harder20*, Claudia Haferlach, MD5, Heike Pfeifer21*, Nicola Goekbuget, MD22, Monika Brüggemann1,2* and Claudia D Baldus, MD1,2*

1Medical Department II, University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
2Clinical Research Unit CATCH ALL (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Kiel, Germany
3Medical Department II, University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, DEU
4University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, DEU
5MLL Munich Leukemia Laboratory, Munich, Germany
6Department of Psychiatry and Psychotherapy, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
7Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, DEU
8Department of Psychiatry and Psychotherapy, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, DEU
9Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
10Institute for Clinical Molecular Biology, Kiel University, Kiel, Germany
11Klinikum Rechts der Isar der TU München, Munich, Germany
12University Hospital Hamburg-Eppendorf, Hamburg, DEU
13Department of Hematology and Oncology, Unversity Hospital Frankfurt, Frankfurt, Frankfurt am Main, Germany
14Department of Medicine A/Hematology and Oncology, University of Muenster, Münster, Germany
15Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Tuebingen, Germany
16Department of Hematology, Oncology and Tumor Immunology (Campus Benjamin Franklin), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany., Berlin, Germany
17University Hospital Schleswig Holstein, Department of Psychiatry and Psychotherapy, Kiel, Germany
18Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
19Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
20Institut für Tumorgenetik Nord, Kiel, Germany
21Department of Medicine II, Hematology/Oncology, Goethe University Hospital, Frankfurt/M., Frankfurt/M., Germany
22Department of Medicine II, Hematology/Oncology, Goethe University Hospital, Frankfurt, Germany

Two developmental trajectories are acknowledged in BCR::ABL1-positive acute lymphoblastic leukemia (ALL) as distinct diagnostic entities by the ICC classification: ‘lymphoid-only’ with BCR::ABL1 restricted to the leukemic B precursor compartment vs. ‘multilineage’ with BCR::ABL1 involvement also in other hematopoietic lineages. Diagnostic standards for establishing this distinction are lacking and associated biological and clinical features are insufficiently characterized.

To establish developmental trajectories, biological phenotypes, and clinical impact we analyzed n=277 BCR::ABL1-positive ALL patients (age: 2-84 years, median: 46) including our GMALL reference data set (n=113) and two independent validation cohorts (MLL: n=61; St Jude’s: n=103; Gu Z, et al. Nat Genet. 2019).

Unsupervised gene expression analysis (RNA-Seq: n=277) identified two major gene expression clusters with two further sub-clusters each (Figure A). This clustering was confirmed by a machine learning classifier trained on the GMALL data set which achieved similar grouping of samples in the external validation cohorts. BCR::ABL1-FISH on FACS-sorted bone marrow/peripheral blood samples revealed the presence of BCR::ABL1 in leukemic as well as myeloid cells in n=18/18 samples from the 1st major cluster (termed ‘multilineage’). In the 2nd major cluster (‘lymphoid’), BCR::ABL1 was restricted to the lymphoid lineage in n=13/16 samples (p<0.001), with n=3/16 cases harboring BCR::ABL1-positive myeloid cells at lower frequencies compared to the multilineage cluster. In each cluster, two patients also harbored BCR::ABL1-positive mature B cells. T cells remained BCR::ABL1-negative. Diagnostic FACS data and analysis of proximity to normal human lymphoid gene expression confirmed more frequent myeloid co-expression and higher proximity to normal pro-B cells in the multilineage cluster, whereas lymphoid cases had increased lymphoid surface marker expression and a stronger proximity to normal pre-B I cells. Genomic profiling using WGS/SNParrays (n=160) revealed significant enrichment for genomic events in the four gene expression sub-clusters: focal deletions comprising exons 1 and 2 of HBS1-like translational GTPase (HBS1L) or monosomy 7 were strongly enriched in the two multilineage sub-clusters (‘delHBS1L’; n=20/27 vs. n=3/133 in remaining cohort or ‘del7’; n=16/25 vs. n=10/135; p<0.001). Remarkably, a novel alternative HBS1L transcript with a putative TSS in intron 3 was highly expressed in both multilineage sub-clusters but not in BCR::ABL1 negative ALL cases or healthy B lymphoid progenitors, suggesting this transcript as novel cooperating event in multilineage BCR::ABL1-positive ALL. One lymphoid sub-cluster was enriched for homozygous deletions in IKZF1 (‘IKZF1’; n=11/55 vs. n=4/105; p=0.008), whereas the other was enriched for homozygous CDKN2A/B deletions (n=21/53 vs. n=3/107; p<0.001) and PAX5 deletions (n=33/53 vs n=26/107; p<0.001; ‘CDKN2A/PAX5’). Hyperdiploid karyotypes were exclusive to the lymphoid main cluster, mostly in CDKN2A/PAX5.

We analyzed the clinical implications of these newly established BCR::ABL1-positive ALL subtypes in our homogenously treated GMALL adult patient cohort (n=98, first diagnosis 2014-2021) including TKI treatment combined with age-adapted chemotherapy, MRD monitoring and allo-SCT in 1st CR (n=84/98, 86%). Overall survival (OS) at 3 years was uniformly high in multilineage and lymphoid cases (70%±6% vs. 70%±8%; p=0.890; Figure B). However, analysis of the sub-clusters revealed an inferior 3-years OS for the IKZF1-/- enriched cluster in contrast to excellent outcome in hyperdiploid cases and intermediate outcomes in the remaining sub-clusters (Figure B).

These data highlight that transcriptomic signatures in BCR::ABL1-positive ALL are driven by developmental disease origins (‘lymphoid’ vs. ‘multilineage’) and specific patterns of corresponding genomic events. Novel molecular subtypes of BCR::ABL1-positive ALL have distinct outcomes in the context of current GMALL treatment protocols. Gene-expression based subtype definitions enable classification of BCR::ABL1-positive ALL according to ICC definitions based on RNA-Seq data alone. These definitions have been implemented in ALLCatchR – our freely available tool for ALL subtype allocation – to facilitate validation and application in clinical diagnostics.

Disclosures: Bastian: BeiGene: Other: Travel Honoraria. Bendig: Amgen: Research Funding. Walter: MLL Munich Leukemia Laboratory: Current Employment. Fiedler: Clinigen: Consultancy; Stemline: Consultancy; Morphosis: Consultancy; Servier: Consultancy, Other: Support for meeting attendance; AbbVie: Consultancy, Honoraria, Other: Support in medical writing; Pfizer: Consultancy; Amgen: Consultancy, Other: Support for meeting attendance, Patents & Royalties; Jazz Pharmaceuticals: Consultancy, Other: Support for meeting attendance; Apis: Research Funding. Schwartz: Pfizer: Consultancy, Honoraria; Amgen: Other: Advosory Board; Protherics: Research Funding. Cario: Servier, Amgen: Research Funding; JazzPharma: Speakers Bureau. Harder: Jazz Pharmaceuticals: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria. Haferlach: MLL Munich Leukemia Laboratory: Current Employment, Other: Equity Ownership. Goekbuget: Servier: Honoraria, Research Funding; Clinigen: Honoraria, Research Funding; Autolus: Honoraria; Incyte: Honoraria, Research Funding; Jazz: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Novartis: Research Funding; Gilead: Honoraria, Research Funding; Amgen: Honoraria, Research Funding. Baldus: Gilead: Consultancy; Jazz Pharmaceuticals: Consultancy; Astellas: Consultancy; BMS: Consultancy; AstraZeneca: Consultancy; Amgen: Consultancy; Jannsen: Consultancy.

*signifies non-member of ASH